Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19), primarily infects the respiratory and digestive tract. Several studies have indicated the alterations of the bacteria...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-07-01
|
| Series: | Pathogens |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-0817/12/7/944 |
| _version_ | 1797587879974666240 |
|---|---|
| author | Linlin Xie Liangjun Chen Xinran Li Junying Zhou Hongpan Tian Jin Zhao Zhiqiang Li Yirong Li |
| author_facet | Linlin Xie Liangjun Chen Xinran Li Junying Zhou Hongpan Tian Jin Zhao Zhiqiang Li Yirong Li |
| author_sort | Linlin Xie |
| collection | DOAJ |
| description | Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19), primarily infects the respiratory and digestive tract. Several studies have indicated the alterations of the bacterial microbiome in the lower respiratory tract during viral infection. However, both bacterial and fungal microbiota in the lung of COVID-19 patients remained to be explored. Methods: In this study, we conducted nanopore sequencing analyses of the lower respiratory tract samples from 38 COVID-19 patients and 26 non-COVID-19 pneumonia controls. Both bacterial and fungal microbiome diversities and microbiota abundances in the lung were compared. Results: Our results revealed significant differences in lung microbiome between COVID-19 patients and non-COVID-19 controls, which were strongly associated with SARS-CoV-2 infection and clinical status. COVID-19 patients exhibited a notably higher abundance of opportunistic pathogens, particularly <i>Acinetobacter baumannii</i> and <i>Candida</i> spp. Furthermore, the potential pathogens enriched in COVID-19 patients were positively correlated with inflammation indicators. Conclusions: Our study highlights the differences in lung microbiome diversity and composition between COVID-19 patients and non-COVID-19 patients. This may contribute to predicting co-pathogens and selecting optimal treatments for respiratory infections caused by SARS-CoV-2. |
| first_indexed | 2024-03-11T00:45:05Z |
| format | Article |
| id | doaj.art-9b11a4fb55bf4244a0a10e522b622289 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-11T00:45:05Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-9b11a4fb55bf4244a0a10e522b6222892023-11-18T20:51:16ZengMDPI AGPathogens2076-08172023-07-0112794410.3390/pathogens12070944Analysis of Lung Microbiome in COVID-19 Patients during Time of HospitalizationLinlin Xie0Liangjun Chen1Xinran Li2Junying Zhou3Hongpan Tian4Jin Zhao5Zhiqiang Li6Yirong Li7Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaDepartment of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaDepartment of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, ChinaBackground: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19), primarily infects the respiratory and digestive tract. Several studies have indicated the alterations of the bacterial microbiome in the lower respiratory tract during viral infection. However, both bacterial and fungal microbiota in the lung of COVID-19 patients remained to be explored. Methods: In this study, we conducted nanopore sequencing analyses of the lower respiratory tract samples from 38 COVID-19 patients and 26 non-COVID-19 pneumonia controls. Both bacterial and fungal microbiome diversities and microbiota abundances in the lung were compared. Results: Our results revealed significant differences in lung microbiome between COVID-19 patients and non-COVID-19 controls, which were strongly associated with SARS-CoV-2 infection and clinical status. COVID-19 patients exhibited a notably higher abundance of opportunistic pathogens, particularly <i>Acinetobacter baumannii</i> and <i>Candida</i> spp. Furthermore, the potential pathogens enriched in COVID-19 patients were positively correlated with inflammation indicators. Conclusions: Our study highlights the differences in lung microbiome diversity and composition between COVID-19 patients and non-COVID-19 patients. This may contribute to predicting co-pathogens and selecting optimal treatments for respiratory infections caused by SARS-CoV-2.https://www.mdpi.com/2076-0817/12/7/944COVID-19SARS-CoV-2lung microbiotananopore sequencing |
| spellingShingle | Linlin Xie Liangjun Chen Xinran Li Junying Zhou Hongpan Tian Jin Zhao Zhiqiang Li Yirong Li Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization Pathogens COVID-19 SARS-CoV-2 lung microbiota nanopore sequencing |
| title | Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization |
| title_full | Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization |
| title_fullStr | Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization |
| title_full_unstemmed | Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization |
| title_short | Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization |
| title_sort | analysis of lung microbiome in covid 19 patients during time of hospitalization |
| topic | COVID-19 SARS-CoV-2 lung microbiota nanopore sequencing |
| url | https://www.mdpi.com/2076-0817/12/7/944 |
| work_keys_str_mv | AT linlinxie analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization AT liangjunchen analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization AT xinranli analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization AT junyingzhou analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization AT hongpantian analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization AT jinzhao analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization AT zhiqiangli analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization AT yirongli analysisoflungmicrobiomeincovid19patientsduringtimeofhospitalization |